5M2M: Complex between human TNF alpha and Llama VHH3

Complex between human TNF alpha and Llama VHH3. Determined by X-ray diffraction at 2.3 Å resolution. Released 30 Aug 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Lama glama
Chains: 12
Atoms: 13,516
Mol. weight: 189.4 kDa
Released: 30 Aug 2017

Explore 5M2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M2M contains 30 α-helices and 141 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, C, G and I: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	28-29	2	1
β-strand	36-38	3	1
β-strand	42-43	2	2
β-strand	48-49	2	2
α-helix	50	1
β-strand	54-67	14	1
β-strand	76-83	8	2
β-strand	90-98	9	2
α-helix	104-106	3
β-strand	113-126	14	1
β-strand	131-136	6	2
α-helix	139-141	3
β-strand	142	1	1
β-strand	151-156	6	1

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-12	3	8
β-strand	18-24	7	7
α-helix	25	1
β-strand	37-44	8	8
β-strand	51-57	7	8
β-strand	63-65	3	8
β-strand	73-78	6	7
β-strand	83-88	6	7
α-helix	93-95	3
β-strand	97-105	9	8
α-helix	113-115	3
β-strand	118-119	2	8
β-strand	123-127	5	8

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-12	3	10
β-strand	18-24	7	9
β-strand	37-44	8	10
β-strand	51-57	7	10
β-strand	63-65	3	10
β-strand	73-78	6	9
β-strand	83-88	6	9
α-helix	93-95	3
β-strand	97-105	9	10
α-helix	113-115	3
β-strand	118-119	2	10
β-strand	123-127	5	10

Chain F: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	18-24	7	11
α-helix	25	1
β-strand	37-44	8	12
β-strand	51-57	7	12
β-strand	63-65	3	12
β-strand	70	1	11
β-strand	73-78	6	11
β-strand	83-88	6	11
α-helix	93-95	3
β-strand	97-105	9	12
α-helix	113-115	3
β-strand	118-119	2	12
β-strand	123-127	5	12

Chains H, J and N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-12	3	16
β-strand	18-24	7	15
β-strand	37-44	8	16
β-strand	51-57	7	16
β-strand	63-65	3	16
β-strand	70	1	15
β-strand	73-78	6	15
β-strand	83-88	6	15
α-helix	93-95	3
β-strand	97-105	9	16
α-helix	113-115	3
β-strand	118-119	2	16
β-strand	123-127	5	16

Chain M: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	21
β-strand	28-29	2	21
β-strand	36-38	3	21
β-strand	42-43	2	22
β-strand	48-49	2	22
α-helix	50	1
β-strand	54-67	14	21
β-strand	76-83	8	22
β-strand	90-98	9	22
β-strand	113-126	14	21
β-strand	131-136	6	22
β-strand	151-156	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C, G, I, M	protein	157	Homo sapiens	P01375 (AlphaFold model)
Llama nanobody VHH3	D, E, F, H, J, N	protein	129	Lama glama

Sequence of entity 1 (A, B, C, G, I, M), FASTA

>5M2M_1 Tumor necrosis factor (chains A, B, C, G, I, M)
VRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYL
GGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Sequence of entity 2 (D, E, F, H, J, N), FASTA

>5M2M_2 Llama nanobody VHH3 (chains D, E, F, H, J, N)
QVQLQESGGGLVQPGGSLRLSCAASGRTFSDHSGYTYTIGWFRQAPGKEREFVARIYWSS
GNTYYADSVKGRFAISRDIAKNTVDLTMNNLEPEDTAVYYCAARDGIPTSRSVESYNYWG
QGTQVTVSS

Primary citation

Bivalent Llama Single-Domain Antibody Fragments against Tumor Necrosis Factor Have Picomolar Potencies due to Intramolecular Interactions. Beirnaert, E., Desmyter, A., Spinelli, S. et al. Front Immunol (2017) 8:867-867. DOI 10.3389/fimmu.2017.00867 · PubMed

Other PDB entries of the same protein (UniProt P01375 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OJO 1.36 Å, Crystal structure of TNF alpha in complex with compound 1
5UUI 1.4 Å, Crystal Structure of Spin-Labeled T77C TNFa
4Y6O 1.6 Å, Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
2E7A 1.8 Å, TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity
4TSV 1.8 Å, High resolution crystal structure of a human tnf-alpha mutant
9OJS 1.85 Å, Crystal structure of TNF alpha in complex with compound 4
5M2J 1.9 Å, Complex between human TNF alpha and Llama VHH2
9BN7 1.92 Å, X-ray crystal structure of TNFa-VNAR C4 complex
2AZ5 2.1 Å, Crystal Structure of TNF-alpha with a small molecule inhibitor
3L9J 2.1 Å, Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal…
7JRA 2.1 Å, HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}qui…
5M2I 2.15 Å, Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1

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